Protein-protein interaction is an important way through which proteins carry out their function(s). Currently, there are several methods to detect protein-protein interactions. Among them, co-immunoprecipitation (Harlow and Lane, 1988, Antibodies, a laboratory manual. Cold Spring Harbor Laboratory), yeast two-hybrid screening (Fields and Song, 1989, Nature, 340:245-246) and phage display library screening (Smith, 1985, Science 228:1315-1317) are the most commonly used. However, there are severe limitations in these methods. In co-immunoprecipitation, a protein of interest can be precipitated with its antibody, which is immobilized on beads. Any other protein(s) that co-immunoprecipitated with the protein of interest can be identified by either blotting with its antibody when it is known or purification and sequencing when it is a novel protein. However, this method cannot be applied to large-scale screening of protein-protein interactions.
Yeast two-hybrid screening is a recently developed technique for detecting protein-protein interaction. Although a single yeast two-hybrid screening assay can detect many interacting proteins, it is prone to false positive and false negative results. Moreover, many protein-protein interactions only occur in the presence of additional cellular factors or after posttranslational modifications, which may not be present in yeast. Therefore, yeast two-hybrid screens fails to identify many important protein-protein interactions that only take place in mammalian cells. Phage display screening of protein-protein interaction suffers similar limitations.
Therefore, there is a need in both basic research and clinical medicine for improved techniques, particularly high-throughput techniques, which allow rapid and detailed analysis of multiple proteins and their interactions. Such techniques would be extremely valuable in monitoring the overall patterns of protein expression, protein posttranslational modification, and protein-protein interaction in different cell types or in the same cell type under different physiological or pathological conditions.